Prof Rosie Woodroffe of the Zoological Society of London uses an electronic collar to track a badger and gain a better understanding of its behaviour and contact with cattle. Photograph: David Chapman

"It's very hard to count an animal that lives underground and only comes out at night," says Prof Rosie Woodroffe, standing in the fresh earth strewn outside a foot-wide hole in a Cornish cattle field. "Badgers love digging," she observes, among the brambles and elders that thrive on the disturbed ground.

Below stone tors and with the salty smell of the sea in the air, Woodroffe is doing what she has done for much of the past 15 years: trapping badgers for science. "The badgers are fat this year," she says. "The wet spring means there's lots of earthworms." But a dry summer could mean four in every five cubs die, she warns, and it is uncertainties in population like these that mean she is seriously worried about the controversial badger culls due to start after 1 June.

The culls are intended to curb the rise of bovine tuberculosis: more than 37,000 cattle were slaughtered in 2012, at a cost to the taxpayer of £100m. But farmers in the pilot cull areas in Gloucestershire and Somerset have to tread a fine line: kill too many badgers and they will break the law against local extinctions of the protected animal, while killing too few means escaping badgers will spread TB even further. The problem, says Woodroffe, is the real number of badgers is hard to establish. Initial estimates were made by counting badger setts.

"This is a stupid way to count badgers," says Woodroffe. "A single sett is not meaningful for a badger because they live in social groups and use more than one sett, possibly four or five."

Initial sett-based estimates from farmers were rejected by the government, which then did its own sett survey, which came up with much higher numbers and derailed the start of the cull in October. The new government data, partly based on DNA testing of badger hair samples, lowered the numbers again.

The uncertainties are so great, says Woodroffe, that it is "perfectly plausible" that every badger in a cull zone could be killed while at the same time too few badgers were killed to meet the minimum number set by the cull licence.

Prof Tim Coulson, a zoologist at Oxford University and a member of the independent expert group advising ministers on the cull, said: "For most wild species, trying to count the number of animals in a population, if they spent a lot of time underground or roaming over large distances, is extremely difficult."

Further uncertainty comes from claims by anti-cull activists to have sabotaged the hair-snare survey by removing fur from the traps. "We wanted to muck up the count and we definitely succeeded," says Jay Tiernan of the Stop the Cull campaign. "I don't see how we didn't." The government says activist action had no impact on the population estimates, but Woodroffe says the claims do add uncertainty.

The Guardian meets Tiernan in the Somerset cull zone, where he ruefully notes that the steep-sided hills provide a good backstop for the marksmen who will carry out the cull. The former soldier, who acknowledges trespass and criminal damage convictions but denies any involvement with violence, says activists have surveyed the areas and are preparing for action.

"We are stopping the cull with the direct action, not tea and biscuits," he says. "But we condemn harassment and we condemn private property damage. I would not be happy to see a brick thrown through a window. We don't want to look like thugs or look desperate – we are in a good position already. We want as much of middle England behind us as possible."

A large section of the public already is, fronted by rock star Brian May and backed by the RSPCA and others. Their 225,000-strong petition won the first House of Commons debate on the cull in which MPs voted against it. Tiernan's more direct tactic, he says, will be to scare badgers away from shooters and he has ready 150 vuvuzelas and a number of "gizmos" – MP3 players linked to megaphones. "We'll be playing heavy metal like Slayer," he says.

Sixty miles away in Dorset, where a reserve cull zone is being prepared, farmer James Cossins is also concerned about badger numbers. "What's made them dig out here?" he asks, standing in a field over a pile of dirt, yards long andstudded with chalk. "I think it's overpopulation. We definitely have more badgers than 20 years ago."

Cossins, whose 2,200-acre mixed farm is adjacent to the proposed cull zone, has little doubt the 27 cattle he lost to TB caught the disease from badgers. "We are a closed herd," he says. "All our animals are bred on the farm. We very occasionally buy in a stock bull, but only from a known farm and only when fully tested for TB."

The neighbouring farms are mainly arable, so "our cows have very little contact with other cows". He adds: "It is very frustrating and demoralising: we dread every test. I've got nothing against the little furry fellows, but sitting back and doing nothing is not an option. People are at their wits' end."

Cossins is the fifth generation of his family to run the farm and his husbandry has earned a valuable "high herd health status" for his cattle. He acknowledges that past farming industry practices helped spread TB, which rose from 235 infections across Britain in 1986 to 28,541 in 2010.

"The movement of cattle in the past did make TB worse, but now that is controlled and I don't know how much tougher you could get. All the rules and regulations are loaded one way: we feel we have all these controls on the cattle but no controls on the badgers."

This is contested by John Bourne, the vet who led the government's 10-year, £50m trial of badger culling which reported in 2008 that it could "make no meaningful contribution" to curbing bovine TB. "The cattle controls in operation at the moment are totally ineffective," he says, because the tuberculin test used is not very accurate, meaning herds can often test negative even while still harbouring the disease.

"It's an absolute nonsense that farmers can move cattle willy-nilly after only two tests. Why won't politicians implement proper cattle movement controls? Because they don't want to upset farmers."

Bourne acknowledges that cattle can get TB from badgers, but says the true problem is the other way around: "Badger infections are following, not leading, TB infections in cattle."

Bourne oversaw the culling of 11,000 badgers in the trial and says it is very hard to cull quickly and effectively, even without interruptions from protesters. "You just chase the badgers around, which makes TB worse," he says. "We don't know what the outcome of the cull pilots will be but the likelihood is it's going to make things worse."Many cull opponents cite vaccination of badgers, or in future of cattle, as a better alternative. But the government's chief veterinary officer, Nigel Gibbens, says: "That is not with us now – the need to control TB in cattle is with us right now. It is a very significant disease causing significant pain."

He is supported by Peter Kendall, the president of the National Farmers Union. "Farmers are doing all they can to stop their cattle from catching bovine TB and vaccination of cattle and badgers is emphatically not an alternative to controlling disease in badgers," he says. He believes a suitable cattle vaccine is too far off and badger vaccination is too expensive.

Woodroffe disagrees. Badgers can be vaccinated now – the Welsh government has chosen this option in preference to culling – and using volunteers could significantly reduce costs, she says. The cull risks being a costly diversion. "If you think about how long the cull policy has taken, the government could have been much further forward with vaccination."

With his glossy black cows pressing in around him, Cossins considers the future. "It may be that culling doesn't work and then we'll have to look at alternatives. In an ideal world I would vaccinate our cows."